biopipen 0.21.0__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/scripts/tcr/Immunarch-diversity.R

@@ -1,60 +1,33 @@
-# Diversity estimation
+
 # https://immunarch.com/articles/web_only/v6_diversity.html
 
-# Other variables are loaded in the parent template
-# immdata is already loaded, meta is mutated
-div_method = {{envs.divs.method | r}}
-div_by = {{envs.divs.by | r}}
-div_order = {{envs.divs.order | r}}
-div_args = {{envs.divs.args | r: todot="-"}}
-div_test = {{envs.divs.test | r}}
-div_cases = {{envs.divs.cases | r: todot="-"}}
-div_devpars = {{envs.divs.devpars | r}}
-div_separate_by = {{envs.divs.separate_by | r}}
-div_align_x = {{envs.divs.align_x | r}}
-div_align_y = {{envs.divs.align_y | r}}
-div_subset = {{envs.divs.subset | r}}
-div_log = {{envs.divs.log | r}}
-div_ncol = {{envs.divs.ncol | r}}
-div_ymin = {{envs.divs.ymin | r}}
-div_ymax = {{envs.divs.ymax | r}}
+log_info("")
+log_info("# Diversity estimation")
+log_info("-----------------------------------")
+
+div_test = div_test %||% list(method = "none", padjust = "none")
+div_devpars = div_devpars %||% list(res = 100, width = 800, height = 800)
 
 div_dir = file.path(outdir, "diversity")
 dir.create(div_dir, showWarnings = FALSE)
 
-print("- Diversity estimation ...")
-
 # Fill up the cases
-update_case = function(case) {
-    if (is.null(case$subset)) {
-        case$subset = div_subset
-    }
-    if (is.null(case$method)) {
-        case$method = div_method
-    }
-    if (is.null(case$by)) {
-        case$by = div_by
-    }
+update_case = function(case, name) {
+    log_debug("Filling up case: {name} ...")
+    case$subset <- case$subset %||% div_subset
+    case$method <- case$method %||% div_method
+    case$by <- case$by %||% div_by
     if (!is.null(case$by) && nchar(case$by) > 0) {
         case$by = unlist(strsplit(case$by, ",")) %>% trimws()
     }
-    if (is.null(case$order)) {
-        case$order = div_order
-    }
-    if (is.null(case$args)) {
-        case$args = div_args
-    }
+    case$plot_type <- case$plot_type %||% div_plot_type
+    case$order <- case$order %||% div_order
+    case$args <- case$args %||% div_args
     for (name in names(case$args)) {
-        if (is.null(case$args[[name]])) {
-            case$args[[name]] = div_args[[name]]
-        }
-    }
-    if (is.null(case$test)) {
-        case$test = div_test
-    }
-    if (is.null(case$test$method)) {
-        case$test$method = div_test$method
+        case$args[[name]] = case$args[[name]] %||% div_args[[name]]
     }
+    case$test <- case$test %||% div_test
+    case$test$method <- case$test$method %||% div_test$method
     if (!case$test$method %in% c("none", "t.test", "wilcox.test")) {
         stop(paste0(
             "Diversity estimation: Unknown test method: ",
@@ -62,46 +35,27 @@ update_case = function(case) {
             ". Expected: t.test, wilcox.test"
         ))
     }
-    if (is.null(case$test$padjust)) {
-        case$test$group = div_test$padjust
-    }
-    if (is.null(case$devpars)) {
-        case$devpars = div_devpars
-    }
-    if (is.null(case$devpars$res)) {
-        case$devpars$res = div_devpars$res
-    }
-    if (is.null(case$devpars$width)) {
-        case$devpars$width = div_devpars$width
-    }
-    if (is.null(case$devpars$height)) {
-        case$devpars$height = div_devpars$height
-    }
-    if (is.null(case$separate_by)) {
-        case$separate_by = div_separate_by
-    }
-    if (is.null(case$align_x)) {
-        case$align_x = div_align_x
-    }
-    if (is.null(case$align_y)) {
-        case$align_y = div_align_y
-    }
-    if (is.null(case$log)) {
-        case$log = div_log
-    }
-    if (is.null(case$ncol)) {
-        case$ncol = div_ncol
-    }
-    if (is.null(case$ymin)) {
-        case$ymin = div_ymin
-    }
-    if (is.null(case$ymax)) {
-        case$ymax = div_ymax
-    }
+    case$test$padjust <- case$test$padjust %||% div_test$padjust
+    case$devpars <- case$devpars %||% div_devpars
+    case$devpars$res <- case$devpars$res %||% div_devpars$res
+    case$devpars$width <- case$devpars$width %||% div_devpars$width
+    case$devpars$height <- case$devpars$height %||% div_devpars$height
+    case$separate_by <- case$separate_by %||% div_separate_by
+    case$split_by <- case$split_by %||% div_split_by
+    case$split_order <- case$split_order %||% div_split_order
+    if (!is.null(case$separate_by) && !is.null(case$split_by)) {
+        stop("Diversity estimation: `separate_by` and `split_by` cannot be specified at the same time")
+    }
+    case$align_x <- case$align_x %||% div_align_x
+    case$align_y <- case$align_y %||% div_align_y
+    case$log <- case$log %||% div_log
+    case$ncol <- case$ncol %||% div_ncol
+    case$ymin <- case$ymin %||% div_ymin
+    case$ymax <- case$ymax %||% div_ymax
     if (!is.null(case$args) && length(case$args) > 0) {
         names(case$args) = paste0(".", names(case$args))
     }
-    if (!is.null(case$test) && case$test != "none" && (is.null(case$by) || length(case$by) == 0)) {
+    if (!is.null(case$test) && case$test$method != "none" && (is.null(case$by) || length(case$by) == 0)) {
         stop("For diversity estimation, `test` is only supported when `by` is specified")
     }
     # Just ignore them for rarefraction
@@ -114,33 +68,16 @@ update_case = function(case) {
     return (case)
 }
 
-# See https://github.com/immunomind/immunarch/pull/341
-vis.immunr_gini <- function(.data, .by = NA, .meta = NA,
-                            .errorbars = c(0.025, 0.975), .errorbars.off = FALSE,
-                            .points = TRUE, .test = TRUE, .signif.label.size = 3.5, ...) {
-  # repDiversity(..., .method = "gini") generates a matrix
-  .data = data.frame(Sample = rownames(.data), Value = .data[, 1])
-  vis_bar(
-    .data = .data, .by = .by, .meta = .meta,
-    .errorbars = .errorbars, .errorbars.off = .errorbars.off, .stack = FALSE,
-    .points = .points, .test = .test, .signif.label.size = .signif.label.size,
-    .defgroupby = "Sample", .grouping.var = "Group",
-    .labs = c(NA, "Gini coefficient"),
-    .title = "Gini coefficient", .subtitle = "Sample diversity estimation using the Gini coefficient",
-    .legend = NA, .leg.title = NA
-  )
-}
-
 if (is.null(div_cases) || length(div_cases) == 0) {
     if (is.null(div_method) || length(div_method) == 0 || nchar(div_method) == 0) {
         stop("No method is specified for diversity estimation")
     }
-    default_case = update_case(list())
+    default_case = update_case(list(), name = "DEFAULT")
     div_cases = list(x = default_case)
     names(div_cases) = div_method
 } else {
     for (name in names(div_cases)) {
-        div_cases[[name]] = update_case(div_cases[[name]])
+        div_cases[[name]] = update_case(div_cases[[name]], name = name)
     }
 }
 
@@ -161,7 +98,7 @@ filter_div = function(div, samples) {
 #   case: the case with argument to be run
 #   ddir: the directory to save the results
 #   value_col: the column name of the value
-run_general = function(d, case, ddir, value_col = "Value") {
+run_general = function(casename, d, case, ddir, value_col = "Value") {
     args = case$args
     args$.data = d$data
     args$.method = case$method
@@ -188,6 +125,14 @@ run_general = function(d, case, ddir, value_col = "Value") {
         )
     }
 
+    if (!is.null(case$split_by)) {
+        newdiv = newdiv %>% left_join(
+            d$meta[, c("Sample", case$split_by), drop = FALSE],
+            by = "Sample",
+            suffix = c(".div", "")
+        )
+    }
+
     write.table(
         newdiv,
         file = file.path(ddir, "diversity.txt"),
@@ -197,18 +142,41 @@ run_general = function(d, case, ddir, value_col = "Value") {
         col.names = TRUE
     )
 
+    .meta_vals <- function(meta, cols) {
+        if (length(cols) == 1) {
+            return (meta[[cols]])
+        }
+
+        vlist = lapply(cols, function(.x) meta[[.x]])
+        do.call(function(...) paste(..., sep = "; "), vlist)
+    }
+
     # plot
     #  by, order, separate_by, align_y
     n_seps = 1
     if (!is.null(case$by) && length(case$by) > 0) {
         if (!is.null(case$separate_by)) {
             metas = split(d$meta, d$meta[[case$separate_by]])
+            if (!is.null(case$split_order)) {
+                if (is.character(case$split_order) && length(case$split_order) == 1) {
+                    case$split_order = trimws(unlist(strsplit(case$split_order, ",")))
+                }
+                metas = metas[intersect(case$split_order, names(metas))]
+            }
             ps = lapply(metas, function(meta) {
-                .test = length(unique(meta[[case$by]])) > 1
-                p = vis(filter_div(div, meta$Sample), .by = case$by, .meta = meta, .test = .test)
-                p = p + ggtitle(paste0(p$labels$title, " (" , case$separate_by, ": ", meta[[case$separate_by]][1], ")"))
+                .test = length(unique(.meta_vals(meta, case$by))) > 1
+                p = vis(
+                    filter_div(div, meta$Sample),
+                    .by = case$by,
+                    .meta = meta,
+                    .test = .test,
+                    .plot.type = case$plot_type
+                )
+                p = p + xlab(paste0(case$separate_by, ": ", meta[[case$separate_by]][1], ")"))
                 if (!is.null(case$order) && length(case$order) > 0) {
-                    p = p + scale_x_discrete(limits = intersect(case$order, unique(meta[[case$by]])))
+                    p = p + scale_x_discrete(
+                        limits = intersect(case$order, unique(.meta_vals(meta, case$by)))
+                    )
                 }
                 if (!is.null(case$ymin) && !is.null(case$ymax)) {
                     p = p + ylim(c(case$ymin, case$ymax))
@@ -222,20 +190,79 @@ run_general = function(d, case, ddir, value_col = "Value") {
             })
             n_seps = length(ps)
             p = wrap_plots(ps, ncol = case$ncol)
+        } else if (!is.null(case$split_by)) {
+            metas = split(d$meta, d$meta[[case$split_by]])
+            if (!is.null(case$split_order)) {
+                if (is.character(case$split_order) && length(case$split_order) == 1) {
+                    case$split_order = trimws(unlist(strsplit(case$split_order, ",")))
+                }
+                metas = metas[intersect(case$split_order, names(metas))]
+            }
+            .i = 0
+            ps = lapply(metas, function(meta) {
+                nby = length(unique(.meta_vals(meta, case$by)))
+                p = vis(
+                    filter_div(div, meta$Sample),
+                    .by = case$by,
+                    .meta = meta,
+                    .test = nby > 1,
+                    .plot.type = case$plot_type
+                )
+                if (!is.null(case$order) && length(case$order) > 0) {
+                    p = p + scale_x_discrete(
+                        limits = intersect(case$order, unique(.meta_vals(meta, case$by)))
+                    )
+                }
+                p = p + xlab(meta[[case$split_by]][1]) + theme(
+                    axis.text.x = element_blank(),
+                    plot.title = element_blank(),
+                    plot.subtitle = element_blank(),
+                    legend.position = "right"
+                )
+                if (.i > 0) {
+                    p = p + theme(
+                        axis.text.y = element_blank(),
+                        axis.title.y = element_blank(),
+                        axis.ticks.y = element_blank(),
+                        axis.line.y = element_blank()
+                    )
+                }
+                .i <<- .i + 1
+                list(
+                    p = p,
+                    ymin = case$ymin %||% min(newdiv[[value_col]]),
+                    ymax = case$ymax %||% max(newdiv[[value_col]]),
+                    nby = nby
+                )
+            })
+            n_seps = length(ps)
+            ymin = do.call(min, lapply(ps, function(x) x$ymin))
+            ymin = max(0, ymin - 0.1)
+            ymax = do.call(max, lapply(ps, function(x) x$ymax))
+            ymax = ymax + 0.3 * (ymax - ymin)  # for the pvalue marks
+            widths = sapply(ps, function(x) ifelse(x$nby == 1, 1.2, x$nby))
+            plots = lapply(ps, function(x) x$p + ylim(c(ymin, ymax)))
+            p = wrap_plots(plots, widths = widths, guides = "collect")
         } else {
-            .test = length(unique(d$meta[[case$by]])) > 1
-            p = vis(div, .by = case$by, .meta = d$meta, .test = .test)
+            .test = length(unique(.meta_vals(d$meta, case$by))) > 1
+            p = vis(div, .by = case$by, .meta = d$meta, .test = .test, .plot.type = case$plot_type)
             if (!is.null(case$order) && length(case$order) > 0) {
-                p = p + scale_x_discrete(limits = intersect(case$order, unique(d$meta[[case$by]])))
+                p = p + scale_x_discrete(limits = intersect(case$order, unique(.meta_vals(d$meta, case$by))))
             }
         }
     } else if (!is.null(case$separate_by)) {
         metas = split(d$meta, d$meta[[case$separate_by]])
+        if (!is.null(case$split_order)) {
+            if (is.character(case$split_order) && length(case$split_order) == 1) {
+                case$split_order = trimws(unlist(strsplit(case$split_order, ",")))
+            }
+            metas = metas[intersect(case$split_order, names(metas))]
+        }
         ps = lapply(metas, function(meta) {
             p = vis(filter_div(div, meta$Sample))
             p = p + ggtitle(paste0(p$labels$title, " (" , case$separate_by, ": ", meta[[case$separate_by]][1], ")"))
             if (!is.null(case$order) && length(case$order) > 0) {
-                p = p + scale_x_discrete(limits = intersect(case$order, unique(meta[[case$by]])))
+                p = p + scale_x_discrete(limits = intersect(case$order, unique(meta[[Sample]])))
             }
             if (!is.null(case$ymin) && !is.null(case$ymax)) {
                 p = p + ylim(c(case$ymin, case$ymax))
@@ -249,10 +276,57 @@ run_general = function(d, case, ddir, value_col = "Value") {
         })
         n_seps = length(ps)
         p = wrap_plots(ps, ncol = case$ncol)
+    } else if (!is.null(case$split_by)) {
+        metas = split(d$meta, d$meta[[case$split_by]])
+        if (!is.null(case$split_order)) {
+            if (is.character(case$split_order) && length(case$split_order) == 1) {
+                case$split_order = trimws(unlist(strsplit(case$split_order, ",")))
+            }
+            metas = metas[intersect(case$split_order, names(metas))]
+        }
+        .i = 0
+        ps = lapply(metas, function(meta) {
+            nby = length(unique(meta$Sample))
+            p = vis(filter_div(div, meta$Sample))
+            if (!is.null(case$order) && length(case$order) > 0) {
+                p = p + scale_x_discrete(limits = intersect(case$order, unique(meta[[Sample]])))
+            }
+            p = p + xlab(meta[[case$split_by]][1]) + theme(
+                axis.text.x = element_blank(),
+                plot.title = element_blank(),
+                plot.subtitle = element_blank(),
+                legend.position = "right"
+            )
+            if (.i > 0) {
+                p = p + theme(
+                    axis.text.y = element_blank(),
+                    axis.title.y = element_blank(),
+                    axis.ticks.y = element_blank(),
+                    axis.line.y = element_blank()
+                )
+            }
+            .i <<- .i + 1
+            list(
+                p = p,
+                ymin = case$ymin %||% min(newdiv[[value_col]]),
+                ymax = case$ymax %||% max(newdiv[[value_col]]) + 0.1 * max(newdiv[[value_col]]),
+                nby = nby
+            )
+        })
+        n_seps = length(ps)
+        ymin = do.call(min, lapply(ps, function(x) x$ymin))
+        ymin = max(0, ymin - 0.1)
+        ymax = do.call(max, lapply(ps, function(x) x$ymax))
+        ymax = ymax + 0.3 * (ymax - ymin)  # for the pvalue marks
+        widths = sapply(ps, function(x) ifelse(x$nby == 1, 1.2, x$nby))
+        plots = lapply(ps, function(x) x$p + ylim(c(ymin, ymax)))
+        p = wrap_plots(plots, widths = widths, guides = "collect")
     } else {
         p = vis(div)
         if (!is.null(case$order) && length(case$order) > 0) {
-            p = p + scale_x_discrete(limits = intersect(case$order, unique(d$meta[[case$by]])))
+            p = p + scale_x_discrete(
+                limits = intersect(case$order, unique(.meta_vals(d$meta, case$by)))
+            )
         }
     }
 
@@ -260,24 +334,97 @@ run_general = function(d, case, ddir, value_col = "Value") {
     width = case$devpars$width
     height = case$devpars$height
     res = case$devpars$res
-    if (is.null(res)) { res = 100 }
+    res = res %||% 100
     if (is.null(height)) {
-        height = if (n_seps == 1) 800 else 600 * ceiling(n_seps / case$ncol)
+        if (!is.nulL(case$split_by)) {
+            height = 800
+        } else {
+            height = if (n_seps == 1) 800 else 600 * ceiling(n_seps / case$ncol)
+        }
     }
     if (is.null(width)) {
         if (!is.null(case$by) && length(case$by) > 0) {
-            width = 200 * length(unique(d$meta[[case$by]])) + 120
+            width = 200 * length(unique(.meta_vals(d$meta, case$by))) + 120
         } else {
             width = 100 * length(unique(d$meta$Sample)) + 120
         }
+        if (!is.null(case$split_by)) { width = width / 2 }
         if (n_seps > 1) {
             width = width * case$ncol
         }
     }
-    png(file.path(ddir, "diversity.png"), width = width, height = height, res = res)
+
+    div_plot = file.path(ddir, "diversity.png")
+    png(div_plot, width = width, height = height, res = res)
     print(p)
     dev.off()
 
+    div_plot_pdf = file.path(ddir, "diversity.pdf")
+    pdf(div_plot_pdf, width = width / res, height = height / res)
+    print(p)
+    dev.off()
+
+    add_report(
+        list(
+            kind = "descr",
+            content = paste0(
+                "Diversity estimation using ",
+                "<code>",
+                case$method,
+                "</code>: ",
+                switch(case$method,
+                    chao1 = paste0(
+                        "a nonparameteric asymptotic estimator of species richness ",
+                        "(number of species in a population)."),
+                    hill = paste0(
+                        "Hill numbers are a mathematically unified family of ",
+                        "diversity indices (differing only by an exponent q)."),
+                    div = paste0(
+                        "true diversity, or the effective number of types, ",
+                        "refers to the number of equally abundant types needed for ",
+                        "the average proportional abundance of the types to equal that ",
+                        "observed in the dataset of interest where all types may ",
+                        "not be equally abundant."),
+                    gini.simp = paste0(
+                        "the Gini-Simpson index is the probability of interspecific ",
+                        "encounter, i.e., probability that two entities represent different types."),
+                    inv.simp = paste0(
+                        "Inverse Simpson index is the effective number of types ",
+                        "that is obtained when the weighted arithmetic mean is used ",
+                        "to quantify average proportional abundance of types in ",
+                        "the dataset of interest."),
+                    gini = paste0(
+                        "the Gini coefficient measures the inequality among ",
+                        "values of a frequency distribution (for example levels of income). ",
+                        "A Gini coefficient of zero expresses perfect equality, ",
+                        "where all values are the same (for example, where everyone has ",
+                        "the same income). A Gini coefficient of one (or 100 percents ) ",
+                        "expresses maximal inequality among values (for example where only ",
+                        "one person has all the income)."),
+                    d50 = paste0(
+                        "the D50 index. ",
+                        "It is the number of types that are needed to cover 50% of the total
+                        abundance.")
+                )
+            )
+        ),
+        h1 = "Diversity Estimation",
+        h2 = casename
+    )
+    add_report(
+        list(
+            name = "Diversity Plot",
+            contents = list(list(kind = "image", src = div_plot, download = div_plot_pdf))
+        ),
+        list(
+            name = "Diversity Table",
+            contents = list(list(kind = "table", src = file.path(ddir, "diversity.txt")))
+        ),
+        h1 = "Diversity Estimation",
+        h2 = casename,
+        ui = "tabs"
+    )
+
     # Test
     if (!is.null(case$test) && case$test$method != "none") {
         # Use pairwise.t.test or pairwise.wilcox.test
@@ -340,6 +487,19 @@ run_general = function(d, case, ddir, value_col = "Value") {
             row.names = FALSE,
             col.names = TRUE
         )
+
+        add_report(
+            list(
+                name = paste0("Test (", case$test$method, ")"),
+                contents = list(list(
+                    kind = "table",
+                    src = file.path(ddir, paste0("diversity.test.", case$test$method, ".txt"))
+                ))
+            ),
+            h1 = "Diversity Estimation",
+            h2 = casename,
+            ui = "tabs"
+        )
     }
 }
 
@@ -406,6 +566,10 @@ run_raref_single = function(d, case, ddir, suffix = "", save_p = TRUE) {
         png(file.path(ddir, "raref.png"), width = devpars$width, height = devpars$height, res = devpars$res)
         print(p)
         dev.off()
+
+        pdf(file.path(ddir, "raref.pdf"), width = devpars$width / devpars$res, height = devpars$height / devpars$res)
+        print(p)
+        dev.off()
     } else {
         return (list(p = p, width = devpars$width))
     }
@@ -421,7 +585,8 @@ run_raref_multi = function(d, case, ddir) {
     widths = list()
     plots = list()
     for (sepvar in sepvars) {
-        print(paste0("  ", case$separate_by, ": ", sepvar))
+        # print(paste0("  ", case$separate_by, ": ", sepvar))
+        log_info("  {case$separate_by}: {sepvar}")
         q = list(include(sepvar))
         names(q) = case$separate_by
         single_run = run_raref_single(
@@ -466,50 +631,103 @@ run_raref_multi = function(d, case, ddir) {
     } else {
         height = case$devpars$height
     }
-    png(file.path(ddir, paste0("raref-", case$separate_by, ".png")), width = width, height = height, res = res)
+    png(
+        file.path(ddir, paste0("raref-", slugify(case$separate_by), ".png")),
+        width = width,
+        height = height,
+        res = res
+    )
+    print(p)
+    dev.off()
+
+    pdf(
+        file.path(ddir, paste0("raref-", slugify(case$separate_by), ".pdf")),
+        width = width / res,
+        height = height / res
+    )
     print(p)
     dev.off()
 }
 
 # Run the diversity estimation for one case
 run_div_case = function(casename) {
-    print(paste0("  Case: ", casename))
+    log_info("Processing case: {casename} ...")
     case = div_cases[[casename]]
     if (case$method == "raref") {
-        ddir = file.path(outdir, "rarefraction", casename)
+        ddir = file.path(outdir, "rarefraction", slugify(casename))
     } else {
-        ddir = file.path(div_dir, casename)
+        ddir = file.path(div_dir, slugify(casename))
     }
     dir.create(ddir, recursive = TRUE, showWarnings = FALSE)
 
     # Filter
     if (!is.null(case$subset)) {
         d = immdata_from_expanded(filter_expanded_immdata(exdata, case$subset))
+        if (nrow(d$meta) == 0) {
+            stop(paste0(
+                "No samples/cells left after filtering. ",
+                "Do you have the correct `subset` for case: ",
+                casename, "?"))
+        }
     } else {
         d = immdata
     }
 
     # Run repDiversity
-    if (case$method == "chao1") {
-        run_general(d, case, ddir, "Estimator")
-    } else if (case$method == "hill") {
-        run_general(d, case, ddir)
-    } else if (case$method == "div") {
-        run_general(d, case, ddir)
-    } else if (case$method == "gini.simp") {
-        run_general(d, case, ddir)
-    } else if (case$method == "inv.simp") {
-        run_general(d, case, ddir)
-    } else if (case$method == "gini") {
-        run_general(d, case, ddir, "V1")
-    } else if (case$method == "raref") {
+    if (case$method == "raref") {
+        add_report(
+            list(
+                kind = "descr",
+                content = paste0(
+                    "Rarefaction is a technique to assess species richness from the ",
+                    "results of sampling through extrapolation. "
+                )
+            ),
+            h1 = "Rarefraction",
+            h2 = casename
+        )
+
         if (!is.null(case$separate_by)) {
             run_raref_multi(d, case, ddir)
+            add_report(
+                list(
+                    kind = "image",
+                    src = file.path(ddir, paste0("raref-", slugify(case$separate_by), ".png")),
+                    download = file.path(ddir, paste0("raref-", slugify(case$separate_by), ".pdf"))
+                ),
+                h1 = "Rarefraction",
+                h2 = casename
+            )
         } else {
             run_raref_single(d, case, ddir)
+            add_report(
+                list(
+                    kind = "image",
+                    src = file.path(ddir, "raref.png"),
+                    download = file.path(ddir, "raref.pdf")
+                ),
+                h1 = "Rarefraction",
+                h2 = casename
+            )
         }
     } else {
-        stop(paste0("Unknown diversity method: ", case$method))
+        if (case$method == "chao1") {
+            run_general(casename, d, case, ddir, "Estimator")
+        } else if (case$method == "hill") {
+            run_general(casename, d, case, ddir)
+        } else if (case$method == "div") {
+            run_general(casename, d, case, ddir)
+        } else if (case$method == "gini.simp") {
+            run_general(casename, d, case, ddir)
+        } else if (case$method == "inv.simp") {
+            run_general(casename, d, case, ddir)
+        } else if (case$method == "gini") {
+            run_general(casename, d, case, ddir, "V1")
+        } else if (case$method == "d50") {
+            run_general(casename, d, case, ddir, "Clones")
+        } else {
+            stop(paste0("Unknown diversity method: ", case$method))
+        }
     }
 }